Article
Biology
Sylvie Estrela, Alicia Sanchez-Gorostiaga, Jean C. C. Vila, Alvaro Sanchez
Summary: The study found that while the family-level community composition can generally be predicted using the null, naturally additive model, there are systematic deviations from the additive predictions that reflect generic patterns of nutrient dominance. Pairs of more similar nutrients tend to be more additive than pairs of dissimilar nutrients, and sugar-acid communities are generally more similar to sugar communities than acid communities, possibly due to family-level asymmetries in nutrient benefits. Overall, the study suggests that regularities in how nutrients interact may help predict community responses to dietary changes.
Article
Biochemistry & Molecular Biology
Denise Martini, Nicolas Dussex, Bruce C. Robertson, Neil J. Gemmell, Michael Knapp
Summary: Climate warming poses a serious threat to alpine species, particularly in limited dispersal environments like islands. Research on the New Zealand kea, the only alpine parrot in the world, suggests that it may not be a true alpine specialist and lacks major genomic differences with its forest adapted sister species, the kaka. Despite this, divergent demographic responses to past climate warming between the species highlight potential future threats to kea survival in a warming world.
Article
Infectious Diseases
Ruichao Li, Yongjia Jiang, Kai Peng, Yanhong Wang, Mianzhi Wang, Yuan Liu, Zhiqiang Wang
Summary: This study confirms the high prevalence of tet(X) in R. anatipestifer. Further investigations are needed to assess the transfer risk of tet(X) from R. anatipestifer to other clinical pathogens.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2022)
Article
Ecology
Alejandra Rodriguez-Verdugo, Martin Ackermann
Summary: The study showed that in a constant commensal environment, two species can coexist, but in a fluctuating environment, one species is likely to go extinct, which was highly deterministic. This extinction was driven by adaptive mutations in a small set of genes.
Article
Environmental Sciences
Yan Li, Xinran Sun, Xia Xiao, Zhiqiang Wang, Ruichao Li
Summary: This study conducted a systematic genomic analysis of 864 tet(X)-positive Escherichia coli isolates worldwide, revealing that China reported the highest number of tet(X)-positive isolates (71.76%), followed by Thailand (8.45%) and Pakistan (5.9%). Pigs, humans, and chickens were identified as important reservoirs of these isolates. The most prevalent clone was the ST10 clone complex, and there was evidence of clonal transmission between ST10 tet(X)-positive isolates and mcr-1-positive but tet(X)-negative human-derived isolates. Cross-contamination between different geographic locations or hosts was also observed. Continuous global surveillance of tet(X)-positive E. coli is therefore crucial in the future.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Environmental Sciences
Xinjun Hu, Yingying Chen, Hao Xu, Jie Qiao, Haoyu Ge, Ruishan Liu, Beiwen Zheng
Summary: This study conducted a prospective investigation in six farms in China and found MCRPEC strains in different samples, with ST10 being the dominant sequence type and the potential for clonal transmission. The results indicated the possibility of interspecies and cross-regional transmission between farms. Therefore, further surveillance and research on non-clinical MCRPEC strains are necessary to reduce their threat.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Biochemistry & Molecular Biology
Wei-Yun Lai, Christian Schloetterer
Summary: The study found that after 100 generations of adaptation to a new laboratory environment, the variance of gene expression in Drosophila simulans males was significantly reduced in 125 and 97 genes, suggesting that the drastic loss in environmental complexity may have triggered selection for reduced variance. This observation could have important implications for studies of adaptation processes in natural and experimental populations.
Article
Biology
Milo S. Johnson, Shreyas Gopalakrishnan, Juhee Goyal, Megan E. Dillingham, Christopher W. Bakerlee, Parris T. Humphrey, Tanush Jagdish, Elizabeth R. Jerison, Katya Kosheleva, Katherine R. Lawrence, Jiseon Min, Alief Moulana, Angela M. Phillips, Julia C. Piper, Ramya Purkanti, Artur Rego-Costa, Michael J. McDonald, Alex N. Nguyen, Michael M. Desai
Summary: Laboratory experimental evolution provides insights into the dynamics of fitness changes over time, revealing patterns of declining adaptability, accumulation of mutations, genetic parallelism, and historical contingency. Unlike long-term evolution in E. coli, yeast populations did not exhibit highly elevated mutation rates or long-term coexistence. Diploid populations in yeast evolution involve fixation of heterozygous mutations and frequent loss-of-heterozygosity events. These results differentiate general features of adaptation across various systems from those specific to individual organisms and environmental conditions.
Article
Biochemistry & Molecular Biology
Karna Gowda, Derek Ping, Madhav Mani, Seppe Kuehn
Summary: The metabolic activities of microbial communities are crucial for the evolution and persistence of life on Earth. This study shows that the dynamics of metabolites in a community can be predicted based on the genes possessed by each member of the community, providing insights into how genome evolution impacts metabolism.
Article
Multidisciplinary Sciences
Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Usman N. Ikumapayi, Golam Sarwar, Catherine Okoi, Peggy-Estelle Maguiagueu Tientcheu, Marianne Defernez, Justin O'Grady, Martin Antonio, Mark J. Pallen
Summary: The study reveals the genomic diversity of Escherichia coli in asymptomatic children from rural Gambia, with 56 genotypes identified and an average of 2.7 genotypes per host. Most diversity is attributed to immigration events, while a minority arises from within-host evolution. Many isolates carry virulence factors and resistance genes, indicating a potential reservoir for these genes. The study also highlights the importance of immigration and strain establishment in generating diversity, with only a minor role played by within-host evolution.
Article
Multidisciplinary Sciences
Leon Faure, Bastien Mollet, Wolfram Liebermeister, Jean-Loup Faulon
Summary: Constraint-based metabolic models have been used to predict microorganism phenotype, but accurate predictions require labor-intensive measurements. We propose hybrid neural-mechanistic models as a machine learning architecture to improve phenotype predictions. Our models outperform constraint-based models with smaller training set sizes, offering a time and resource-saving approach in systems biology and biological engineering projects.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Prince Kumar, Mukesh K. Meghvansi, D. Kamboj
Summary: Shigella has the ability to rapidly develop antibiotic resistance, posing a challenge for dysentery treatment. Phage therapy is an effective alternative for controlling Shigella infections. A newly isolated polyvalent phage 2019SD1 showed lytic activity against multiple bacterial strains and potential biocontrol capabilities.
SCIENTIFIC REPORTS
(2021)
Review
Microbiology
J. Urbaniec, Ye Xu, Y. Hu, S. Hingley-Wilson, J. McFadden
Summary: This review discusses antibiotic persistence, presents the "hunker" theory of persister cell formation based on intrinsic heterogeneity of bacterial growth and metabolism, and emphasizes the urgent need to develop effective anti-persister treatment regimes to combat antimicrobial resistance.
FEMS MICROBIOLOGY REVIEWS
(2022)
Article
Microbiology
Fatma Abdelrahman, Nouran Rezk, Mohamed S. Fayez, Mohamed Abdelmoteleb, Reham Atteya, Mohamed Elhadidy, Ayman El-Shibiny
Summary: This study isolated and characterized three novel bacteriophages against E. coli from sewage water. The phages had a genome size of 44,776 bp and belonged to the Siphoviridae family. They showed good tolerance to a broad range of pH and temperature.
Article
Biology
Margie Kinnersley, Katja Schwartz, Dong-Dong Yang, Gavin Sherlock, Frank Rosenzweig
Summary: This study conducted experimental evolution on Escherichia coli populations and found that in a resource-limited environment, the spectrum of high-frequency beneficial mutations is narrow when mutational input is increased, resulting in many beneficial mutations arising but few fixing. It was also discovered that mutations mainly revolved around genes related to glucose uptake, global regulation, membrane biogenesis, and most mutations remained at a lower frequency within lineages.
Article
Biotechnology & Applied Microbiology
Katherine M. Elston, Julie Perreau, Gerald P. Maeda, Nancy A. Moran, Jeffrey E. Barrick
Summary: This study demonstrates the genetic engineering of a culturable aphid symbiont, Serratia symbiotica CWBI-2.3(T), and its dynamics in colonizing aphid guts across multiple species, as well as its impact on aphid fitness. The results provide insights for developing CWBI-2.3(T) for aphid paratransgenesis, which could advance the study of aphid biology and future agricultural technologies.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Kyle J. Card, Misty D. Thomas, Joseph L. Graves, Jeffrey E. Barrick, Richard E. Lenski
Summary: Antibiotic resistance is a growing health concern, with epistatic interactions between mutations complicating the ability to predict evolution. Differences in genetic backgrounds can lead to idiosyncratic responses in the evolvability of resistance, with lineages founded by different genotypes taking parallel or divergent mutational paths. Historical contingency can alter both genotypic and phenotypic pathways to antibiotic resistance, as evidenced by differences in mutation patterns among different genetic starting points.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Nkrumah A. Grant, Ali Abdel Magid, Joshua Franklin, Yann Dufour, Richard E. Lenski
Summary: The study demonstrates that bacteria evolve larger cells in experimental environments, confirming the ability of cell morphology to evolve and diversify with substantial heterogeneity across replicate lines. Across 50,000 generations, cell size and fitness remain correlated, indicating the beneficial aspect of larger cells and partial compensation for less favorable surface area-to-volume ratios.
JOURNAL OF BACTERIOLOGY
(2021)
Article
Multidisciplinary Sciences
Jessika Consuegra, Joel Gaffe, Richard E. Lenski, Thomas Hindre, Jeffrey E. Barrick, Olivier Tenaillon, Dominique Schneider
Summary: The study shows that IS elements play an important role in bacterial genomic evolution and adaptation, with mutations they cause being either beneficial or harmful. IS-mediated mutations can promote adaptive evolution, but excessive IS activity over time may limit evolutionary possibilities.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Jannell V. Bazurto, Siavash Riazi, Simon D'Alton, Daniel E. Deatherage, Eric L. Bruger, Jeffrey E. Barrick, Christopher J. Marx
Summary: The study investigates how Methylorubrum extorquens responds to formaldehyde with and without the EfgA-formaldehyde-mediated translational response. Functional EfgA allows for a rapid transcriptional response to formaldehyde and its loss leads to heightened proteotoxic and genotoxic stress. Both EfgA-formaldehyde- and kanamycin-mediated translation inhibition share many downstream consequences.
Review
Biochemistry & Molecular Biology
Katherine M. Elston, Sean P. Leonard, Peng Geng, Sarah B. Bialik, Elizabeth Robinson, Jeffrey E. Barrick
Summary: Insects have significant associations with microbes, and genetically engineering insect symbionts is crucial for understanding and utilizing these relationships. Different types of insect-bacteria relationships are summarized, along with the methods used to genetically modify endosymbiont and gut symbiont species. Recent studies have utilized this approach to study symbioses, manipulate insect-microbe interactions, and influence insect biology, offering promise in solving societal challenges like controlling pests and protecting pollinator health.
TRENDS IN MICROBIOLOGY
(2022)
Article
Microbiology
Camilo Gomez-Garzon, Jeffrey E. Barrick, Shelley M. Payne
Summary: Iron acquisition is crucial for living organisms, and the Feo system is the most prevalent bacterial iron transporter. This study examines the evolution of the Feo transporter and suggests that FeoC, one of the accessory proteins, has been lost in many bacterial lineages. Experimental evidence supports the hypothesis that FeoC may have different functions in different species, and its loss is promoted by mutations in FeoA or by the fusion of FeoA and FeoB. The proposed evolutionary model for the Feo system is based on bioinformatic analyses and experimental data.
Review
Biochemistry & Molecular Biology
Ruth Rodriguez-Pastor, Yarden Shafran, Nadav Knossow, Ricardo Gutierrez, Shimon Harrus, Luis Zaman, Richard E. Lenski, Jeffrey E. Barrick, Hadas Hawlena
Summary: This article introduces laboratory experiments on the evolution of blood-borne parasitic microbes in animal hosts, offering guidelines for designing such experiments. The importance of selecting appropriate ancestral genotypes, treatments, replicates, controls, variables, covariates, and timing for checkpoints is emphasized, along with recommended preliminary experiments for quantification and transmission methods. Despite their technical nature, these methodological considerations also have conceptual implications.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Genetics & Heredity
Rohan Maddamsetti, Nkrumah A. Granti
Summary: In this study, a simple test method was introduced to infer positive and purifying selection during the real-time evolution of hypermutator pathogens, and it was validated using metagenomic time series data. The results showed that the test method was able to detect both types of selection in different microbial populations and provided evidence of ongoing positive selection on key regulatory genes.
Article
Biochemistry & Molecular Biology
Gabriel R. Burks, Lehan Yao, Falon C. Kalutantirige, Kyle J. Gray, Elizabeth Bello, Shreyas Rajagopalan, Sarah B. Bialik, Jeffrey E. Barrick, Marianne Alleyne, Qian Chen, Charles M. Schroeder
Summary: This study investigates the structural and mechanical properties of leafhopper brochosomes using a combination of techniques including atomic force microscopy, electron microscopy, electron tomography, and machine learning-based image analysis. The results reveal that brochosomes are rigid hollow spheres with characteristic dimensions and morphologies determined by the leafhopper species. The study also provides insights into the compression modulus of brochosomes, which is consistent with crystalline proteins. These findings contribute to a better understanding of the nanostructured biological materials.
Article
Biochemical Research Methods
Patrick J. Lariviere, Sean P. Leonard, Richard D. Horak, J. Elijah Powell, Jeffrey E. Barrick
Summary: Honey bees are important pollinators and model organisms for studying social behavior, development, and cognition. Researchers have engineered a bee gut bacterium, Snodgrassella alvi, to induce a sustained host RNA interference response that reduces the expression of targeted genes. This method offers a streamlined and scalable approach for studying honey bee biology.
Article
Multidisciplinary Sciences
Katherine M. Elston, Gerald P. Maeda, Julie Perreau, Jeffrey E. Barrick
Summary: This study aimed to adapt a new method called symbiont-mediated RNA interference (smRNAi) for use in aphids. However, under the conditions tested, smRNAi was not a reliable method for aphid gene knockdown.
Article
Ecology
Katherine M. Elston, Laila E. Phillips, Sean P. Leonard, Eleanor Young, Jo-anne C. Holley, Tasneem Ahsanullah, Braydin McReynolds, Nancy A. Moran, Jeffrey E. Barrick
Summary: The Pathfinder toolkit is designed to determine the compatibility of a bacterium with different plasmid components, allowing rapid screening through multiplex conjugation. It also provides foundational genetic tools for studying microbial ecology and host-associated microbes, especially in the gut microbiome of a model insect species.
ISME COMMUNICATIONS
(2023)
Article
Genetics & Heredity
Isaac Gifford, Aurko Dasgupta, Jeffrey E. Barrick
Summary: Sequencing studies revealed a stable intragenomic recombination rate of rRNA gene copies, measured at 3.6 x 10(-4) per genome per generation or 8.6 x 10(-6) per rRNA operon per homologous donor operon per generation.
G3-GENES GENOMES GENETICS
(2021)
Article
Microbiology
Camilo Gomez-Garzon, Jeffrey E. Barrick, Shelley M. Payne
Summary: Feo, a ferrous iron transport system, is critical for virulence in certain bacterial species. The large protein FeoB facilitates iron transport into bacterial cells, while the functions of FeoA and FeoC remain unclear.